protocols::abinitio::abscript::AbscriptStageMover Class Reference

#include <AbscriptStageMover.hh>

Inheritance diagram for protocols::abinitio::abscript::AbscriptStageMover:

Public Member Functions
	AbscriptStageMover (StageID stage, moves::MonteCarloOP mc, core::scoring::ScoreFunctionOP score, core::Size cycles)
void	apply (core::pose::Pose &)
void	yield_submovers (MoverSet &set) const
std::string	get_name () const
	Each derived class must specify its name. The class name. More...
bool	setup_stage (core::pose::Pose &pose, core::Real const &progress)
void	add_submover (ClientMoverOP mover, core::Real weight)
void	add_preparer (StagePreparerOP mover)
void	set_cycles_adjust (core::Real in)
void	set_seq_sep_ramping (core::Real const slope, core::Real const intercept)
void	set_chainbreak_ramping (core::Real const slope, core::Real const intercept)
core::Real const &	seq_sep_intercept ()
core::scoring::ScoreFunctionCOP	scorefxn () const
Public Member Functions inherited from protocols::moves::Mover
	Mover ()
virtual	~Mover ()
virtual MoverSP	create ()
MoverCOP	get_self_ptr () const
MoverOP	get_self_ptr ()
MoverCAP	get_self_weak_ptr () const
MoverAP	get_self_weak_ptr ()
virtual void	apply (core::io::serialization::PipeMap &pmap)
virtual void	parse_state (SerializableState const &state)
virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void	save_state (SerializableState &state)
	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...
	Mover (Mover const &other)
Mover &	operator= (Mover const &other)
	assignment operator More...
virtual core::Real	last_proposal_density_ratio ()
std::string const &	type () const
void	set_type (std::string const &setting)
std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
virtual void	set_current_tag (std::string const &new_tag)
virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...
virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
PoseCOP	get_input_pose () const
PoseCOP	get_native_pose () const
virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
void	type (const std::string &type_in)
virtual MoverOP	clone () const
	Return a clone of the Mover object. More...
virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string	get_type () const
MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...
void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...
virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
virtual Strings &	info ()
	non-const accessor More...
virtual Strings const &	info () const
	const accessor More...
virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const
virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Types
typedef environment::ClientMoverOP	ClientMoverOP
typedef std::set< ClientMoverOP >	MoverSet
typedef std::set< StagePreparerOP >	PreparerSet

Private Member Functions
void	update_max_seq_sep (core::pose::Pose &pose, core::Real const &progress)

Private Attributes
StageID	stage_
moves::RandomMoverOP	random_mover_
MoverSet	movers_
PreparerSet	preparers_
core::Size const	cycles_
core::Real	cycles_adjust_
core::scoring::ScoreFunctionOP	score_
moves::MonteCarloOP	mc_
core::Real	temperature_
core::Real	seqsep_slope_
core::Real	seqsep_intcpt_
core::Real	chbreak_slope_
core::Real	chbreak_intcpt_
constraints_additional::MaxSeqSepConstraintSetOP	constraints_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP
typedef core::pose::Pose	Pose
typedef core::pose::PoseCOP	PoseCOP
typedef protocols::filters::Filters_map	Filters_map
typedef std::list< std::string >	Strings
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()
static void	register_options ()
	Overload this static method if you access options within the mover. More...
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Member Typedef Documentation

typedef environment::ClientMoverOP protocols::abinitio::abscript::AbscriptStageMover::ClientMoverOP

private

typedef std::set< ClientMoverOP > protocols::abinitio::abscript::AbscriptStageMover::MoverSet

private

typedef std::set< StagePreparerOP > protocols::abinitio::abscript::AbscriptStageMover::PreparerSet

private

Constructor & Destructor Documentation

protocols::abinitio::abscript::AbscriptStageMover::AbscriptStageMover	(	StageID	stage,
		moves::MonteCarloOP	mc,
		core::scoring::ScoreFunctionOP	score,
		core::Size	cycles
	)

References random_mover_.

Member Function Documentation

void protocols::abinitio::abscript::AbscriptStageMover::add_preparer

(

StagePreparerOP

mover

)

References preparers_.

void protocols::abinitio::abscript::AbscriptStageMover::add_submover	(	ClientMoverOP	mover,
		core::Real	weight
	)

References movers_, and random_mover_.

void protocols::abinitio::abscript::AbscriptStageMover::apply ( core::pose::Pose &  pose )

virtual

Implements protocols::moves::Mover.

References protocols::moves::RepeatMover::apply(), core::pose::Pose::constraint_set(), cycles_, cycles_adjust_, protocols::abinitio::abscript::I, mc_, random_mover_, and stage_.

Referenced by protocols::abinitio::abscript::AbscriptMover::StageTracker::do_step().

std::string protocols::abinitio::abscript::AbscriptStageMover::get_name ( ) const

virtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References stage_, and core::id::to_string().

core::scoring::ScoreFunctionCOP protocols::abinitio::abscript::AbscriptStageMover::scorefxn ( ) const

inline

References score_.

core::Real const& protocols::abinitio::abscript::AbscriptStageMover::seq_sep_intercept ( )

inline

References seqsep_intcpt_.

void protocols::abinitio::abscript::AbscriptStageMover::set_chainbreak_ramping	(	core::Real const	slope,
		core::Real const	intercept
	)

References chbreak_intcpt_, and chbreak_slope_.

void protocols::abinitio::abscript::AbscriptStageMover::set_cycles_adjust

(

core::Real

in

)

References cycles_adjust_.

void protocols::abinitio::abscript::AbscriptStageMover::set_seq_sep_ramping	(	core::Real const	slope,
		core::Real const	intercept
	)

References seqsep_intcpt_, and seqsep_slope_.

bool protocols::abinitio::abscript::AbscriptStageMover::setup_stage	(	core::pose::Pose &	pose,
		core::Real const &	progress
	)

References protocols::abinitio::abscript::I, mc_, preparers_, score_, protocols::abinitio::abscript::score_cst(), stage_, temperature_, and update_max_seq_sep().

Referenced by protocols::abinitio::abscript::AbscriptMover::StageTracker::do_step().

void protocols::abinitio::abscript::AbscriptStageMover::update_max_seq_sep ( core::pose::Pose &  pose, core::Real const &  progress  )

private

References chbreak_intcpt_, chbreak_slope_, core::pose::Pose::constraint_set(), constraints_, core::scoring::coordinate_constraint, core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep(), core::pose::Pose::fold_tree(), protocols::abinitio::abscript::IVa, protocols::abinitio::abscript::IVb, core::scoring::linear_chainbreak, mc_, core::scoring::overlap_chainbreak, score_, seqsep_intcpt_, seqsep_slope_, stage_, core::pose::Pose::total_residue(), and tr().

Referenced by setup_stage().

void protocols::abinitio::abscript::AbscriptStageMover::yield_submovers

(

MoverSet &

set

)

const

References movers_, and preparers_.

Member Data Documentation

core::Real protocols::abinitio::abscript::AbscriptStageMover::chbreak_intcpt_

private

Referenced by set_chainbreak_ramping(), and update_max_seq_sep().

core::Real protocols::abinitio::abscript::AbscriptStageMover::chbreak_slope_

private

Referenced by set_chainbreak_ramping(), and update_max_seq_sep().

constraints_additional::MaxSeqSepConstraintSetOP protocols::abinitio::abscript::AbscriptStageMover::constraints_

private

Referenced by update_max_seq_sep().

core::Size const protocols::abinitio::abscript::AbscriptStageMover::cycles_

private

Referenced by apply().

core::Real protocols::abinitio::abscript::AbscriptStageMover::cycles_adjust_

private

Referenced by apply(), and set_cycles_adjust().

moves::MonteCarloOP protocols::abinitio::abscript::AbscriptStageMover::mc_

private

Referenced by apply(), setup_stage(), and update_max_seq_sep().

MoverSet protocols::abinitio::abscript::AbscriptStageMover::movers_

private

Referenced by add_submover(), and yield_submovers().

PreparerSet protocols::abinitio::abscript::AbscriptStageMover::preparers_

private

Referenced by add_preparer(), setup_stage(), and yield_submovers().

moves::RandomMoverOP protocols::abinitio::abscript::AbscriptStageMover::random_mover_

private

Referenced by AbscriptStageMover(), add_submover(), and apply().

core::scoring::ScoreFunctionOP protocols::abinitio::abscript::AbscriptStageMover::score_

private

Referenced by scorefxn(), setup_stage(), and update_max_seq_sep().

core::Real protocols::abinitio::abscript::AbscriptStageMover::seqsep_intcpt_

private

Referenced by seq_sep_intercept(), set_seq_sep_ramping(), and update_max_seq_sep().

core::Real protocols::abinitio::abscript::AbscriptStageMover::seqsep_slope_

private

Referenced by set_seq_sep_ramping(), and update_max_seq_sep().

StageID protocols::abinitio::abscript::AbscriptStageMover::stage_

private

Referenced by apply(), get_name(), setup_stage(), and update_max_seq_sep().

core::Real protocols::abinitio::abscript::AbscriptStageMover::temperature_

private

Referenced by setup_stage().

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The documentation for this class was generated from the following files:

• src/protocols/abinitio/abscript/AbscriptStageMover.hh
• src/protocols/abinitio/abscript/AbscriptStageMover.cc